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biotite-dev / biotite

A comprehensive library for computational molecular biology
https://www.biotite-python.org
BSD 3-Clause "New" or "Revised" License
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Trajectory_sse.py: Not working #558

Closed vaibhavanand1 closed 5 months ago

vaibhavanand1 commented 5 months ago

I wanted to plot the secondary structure plot for my simulation trajectories. But first, I tried to execute the given code with the given files. But it is throwing an error at the app.start() step. I suspect it could be due to different versions of python in use. Anyway, I'm trying with other method, but if possible please look into this. Error is -

FileNotFoundError Traceback (most recent call last) Cell In[16], line 5 3 for idx, frame in enumerate(traj): 4 app = DsspApp(traj[idx]) ----> 5 app.start()

File c:\Users\vaibh\anaconda3\Lib\site-packages\biotite\application\application.py:63, in requires_state..decorator..wrapper(*args, *kwargs) 58 if not instance._state & app_state: 59 raise AppStateError( 60 f"The application is in {instance.get_app_state()} state, " 61 f"but {app_state} state is required" 62 ) ---> 63 return func(args, **kwargs)

File c:\Users\vaibh\anaconda3\Lib\site-packages\biotite\application\application.py:118, in Application.start(self) 112 @requires_state(AppState.CREATED) 113 def start(self): 114 """ 115 Start the application run and set its state to RUNNING. 116 This can only be done from the CREATED state. 117 """ --> 118 self.run() 119 self._start_time = time.time() 120 self._state = AppState.RUNNING ... 1553 self._close_pipe_fds(p2cread, p2cwrite, 1554 c2pread, c2pwrite, 1555 errread, errwrite)

FileNotFoundError: [WinError 2] The system cannot find the file specified Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...

padix-key commented 5 months ago

Hi, the error sounds like the dssp software is not installed on your system. All application interfaces in biotite.application depend on some external software, that is not shipped with the package, but must be installed separately.

vaibhavanand1 commented 5 months ago

Hi, Thank you for the reply. Yes I don't have dssp software installed. Although, I managed to plot them using other tools, thanks to your code, it was very helpful. Best, Vaibhav

On Fri, 3 May, 2024, 12:41 pm Patrick Kunzmann, @.***> wrote:

The error sounds like the dssp software is not installed on your system. All application interfaces in biotite.application depend on some external software, that is not shipped with the package, but must be installed separately.

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